[AMBER] set command and VMD

From: Arjun Sharma <arjunsharma83.gmail.com>
Date: Sat, 14 Mar 2015 17:44:23 -0500

Dear Amber users,

 I’m trying to merge two polymer fragments into one. I use “set" command to specify head and tail of two fragments and use “bond” or “sequence” command to combine them. The problem is when I try to visualize this merged fragment in VMD, I see that for some reason VMD considers atom # 1 as atom # 0.

When I try to visualize the bond between say atom 1 and atom 4 of the fragment in VMD, I specify "index 1 4" but I see the bond between the next atoms (between atom 2 and atom 5 ), so to visualize the bond between atom 1 and atom 4, I have to "index 0 3”. Why is that happening ?

My other question is when I use the “set command” in tleap as shown below

>set POLA tail POLA.1.C1
>set POLB head POLB.2.C1
 The value must be of the type: Atom
Why can’t use the POLB fragment as residue 2 since it will be residue 2 in the merged fragment ? It works when I use "set POLB head POLB.1.C1” and PDB file generated from this merger gives me the VMD issue as described above. Are these two issued related ?

 I would greatly appreciate any help.

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Received on Sat Mar 14 2015 - 16:00:03 PDT
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